Contacts of the helix formed by residues 165 - 175 (chain B) in PDB entry 4WMJ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 165 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389A ASN* 6.0 1.0 - - - +
158B ASN* 4.3 5.0 + - - +
160B GLY* 3.4 21.7 - - - +
161B ILE 4.3 2.2 - - - -
162B GLY 2.9 7.9 + - - +
163B GLY 3.2 0.4 - - - -
164B SER* 1.3 78.9 - - - +
166B LEU* 1.3 80.0 + - - +
167B GLY 3.4 2.0 - - - -
168B PRO* 3.4 5.2 - - - +
169B LEU* 3.0 31.8 + - - +
186B PHE* 3.6 26.5 - - - +
187B VAL 4.5 2.3 - - - +
188B SER* 3.5 26.6 + - - -
194B HIS* 5.5 0.2 + - - -
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Residues in contact with LEU 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A ALA* 4.3 12.3 - - + -
162B GLY* 2.9 14.4 + - - +
163B GLY* 5.3 0.7 - - - -
165B ASP* 1.3 87.9 - - - +
167B GLY* 1.3 58.2 + - - +
169B LEU* 3.8 11.0 - - + +
170B MET* 2.9 33.5 + - + +
350B ARG* 5.1 9.6 - - + +
353B ALA* 3.6 39.7 - - + +
354B TYR* 3.9 17.9 - - + +
357B GLN* 3.6 30.1 - - + +
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Residues in contact with GLY 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B GLY* 4.5 5.1 + - - -
166B LEU* 1.3 76.2 - - - +
168B PRO* 1.3 71.8 - - - +
170B MET* 3.2 0.9 + - - -
171B VAL* 2.9 30.0 + - - +
279B LEU* 3.8 15.7 - - - -
354B TYR* 3.3 28.3 - - - -
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Residues in contact with PRO 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B ASN* 4.8 2.0 - - - +
163B GLY 4.2 10.1 - - - +
164B SER 4.1 9.6 - - - +
165B ASP 3.4 11.0 - - - +
167B GLY* 1.3 90.6 - - - +
169B LEU* 1.3 55.6 + - - +
172B THR* 2.9 36.0 + - - +
186B PHE* 3.6 10.8 - - + -
279B LEU* 4.4 5.6 - - + -
283B ILE* 3.7 30.7 - - + +
286B SER* 3.2 24.5 - - - +
287B ILE* 3.9 15.5 - - + -
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Residues in contact with LEU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ASP* 3.0 35.2 + - - +
166B LEU* 3.8 10.5 - - + +
168B PRO* 1.3 76.0 - - - +
170B MET* 1.3 66.8 + - - +
172B THR* 3.2 7.4 + - - -
173B GLU* 3.1 31.6 + - + +
186B PHE* 3.7 28.6 - - + -
350B ARG* 3.7 34.3 - - + +
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Residues in contact with MET 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B LEU* 2.9 18.7 + - + +
167B GLY 3.8 1.8 - - - +
169B LEU* 1.3 84.6 - - + +
171B VAL* 1.3 68.2 + - + +
173B GLU* 3.5 2.3 + - - +
174B ALA* 3.0 33.4 + - + +
347B TYR 4.7 0.7 - - - +
348B LEU* 5.8 1.3 - - - -
350B ARG* 3.4 40.1 + - + +
351B PHE* 3.8 26.0 - - + +
354B TYR* 3.7 35.0 - - + -
490B LEU* 4.8 4.0 - - - -
494B ILE* 3.8 26.5 - - + -
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Residues in contact with VAL 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B GLY 2.9 20.3 + - - +
170B MET* 1.3 84.2 - - - +
172B THR* 1.3 58.9 + - - +
174B ALA* 3.2 3.1 + - - +
175B LEU* 2.8 53.3 + - + +
279B LEU* 4.1 17.7 - - + -
287B ILE* 3.9 27.4 - - + -
299B LEU* 4.2 8.7 - - + -
490B LEU* 4.2 4.5 - - + -
494B ILE* 4.0 26.9 - - + -
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Residues in contact with THR 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B PRO 2.9 25.9 + - - +
169B LEU 3.2 7.6 + - - -
171B VAL* 1.3 75.7 - - - +
173B GLU* 1.3 63.4 + - - +
175B LEU* 3.8 2.2 - - - -
176B LYS* 3.2 18.2 + - - +
184B VAL* 4.3 5.2 - - + +
186B PHE* 3.3 24.9 - - + -
286B SER 4.2 2.5 - - - +
287B ILE* 3.9 28.9 - - + +
290B TYR* 3.4 43.9 - - + -
291B ILE* 5.6 1.3 - - + -
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Residues in contact with GLU 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B LEU* 3.1 37.6 + - + +
170B MET* 3.7 5.8 - - - +
172B THR* 1.3 79.8 + - - +
174B ALA* 1.3 62.0 + - - +
175B LEU 3.4 0.3 + - - -
176B LYS* 3.5 30.0 + - - +
184B VAL* 6.1 1.4 - - - +
186B PHE* 5.9 2.0 - - + -
290B TYR* 5.7 1.0 + - - -
347B TYR* 3.3 19.7 - - - +
349B HIS* 2.8 40.5 + - + +
350B ARG* 5.0 1.8 - - + +
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Residues in contact with ALA 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B MET* 3.0 22.8 + - - +
171B VAL 3.2 4.0 + - - +
173B GLU* 1.3 76.1 - - - +
175B LEU* 1.3 65.3 + - - +
176B LYS 3.4 0.6 + - - -
177B PRO* 4.0 3.6 - - - +
178B TYR* 5.8 0.2 - - - -
347B TYR* 3.3 28.7 + - - +
348B LEU* 3.6 27.8 - - + +
416B HIS* 5.7 1.6 - - - -
485B PHE* 5.2 4.3 - - - +
490B LEU* 3.8 20.6 - - + -
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Residues in contact with LEU 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B VAL* 2.8 36.5 + - + +
172B THR 3.8 3.6 - - - +
174B ALA* 1.3 82.7 - - - +
176B LYS* 1.3 53.3 + - - +
177B PRO* 3.1 5.8 - - - -
178B TYR* 2.8 43.0 + - + +
287B ILE* 5.2 0.2 - - + -
291B ILE* 3.8 34.5 - - + +
299B LEU* 4.7 5.4 - - + -
348B LEU* 6.3 0.2 - - + -
485B PHE* 4.5 5.4 - - + +
486B THR* 3.8 27.8 - - - +
487B PRO* 3.9 22.0 - - + -
490B LEU* 3.8 18.4 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il